QuestionsCategory: ChIP-Seq Data AnalysisControl Types: Is there a reason not to use both IgG and Input controls?
stonelakeak@nih.gov Staff asked 5 months ago

Is there a reason not to use both IgG and Input controls?

1 Answers
stonelakeak@nih.gov Staff answered 5 months ago

There are a few reasons why people don’t tend to use both IgG and input controls, but there is nothing inherently wrong with doing so. First, libraries tend to be expensive so to cut costs people tend to choose one or the other. Second, you can only directly compare your data to one control (especially with peak calling). Finally, since the two controls indicate different kinds of biases, it can often be confusing to think about how to interpret these differences and account for them. – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde